The prison workout works. Also, do one armed pushups. You'll work your obliques and a lot of muscles you didn't think you had, not to mention your balance. Extra points if you can switch between arms Bruce Lee style. And remember, one arm should be behind your back at all times, so this last trick is tough.

I can't do them. But a pretty good example of how the body weight exercises can be leveraged.

Two of the effects of lifting iron that I cannot figure out how to replicate are the really heavy dead lift and the really heavy squat. I want to repeat, I'm a reader now, not a lifter. However, from what I read, it seems that these two done very heavy for few repititions are really worthwhile in putting on some muscle.

ok im no physiologist, but I can speak for myself. I do them slightly different to the pic above, i put a full pushup (done very slowly) into the middle. That guy seems to spring back to the lowest point of the pushup and then kick back up again and jump. I spring back to the highest point of the pushup, do pushup, then kick back up and jump. I find that burpees then give me the benefit of those pushups (multiplied out by descending prison workout sets of 15, thats a bunch of pushups). They give me a very solid lower body workout from the explosive jump at the end from a full squat. Sore pecs, triceps, glutes and quads ensue. I suspect there are a bunch of stabilizer things happening as well. Most important in my case is they really get you puffing - a pretty solid part-cardio part-conditioning thing going on.

That one movement works pretty much the entire body from head to toe by combining a squat with a pushup. Because you're constantly switching from squats to pushups you're teaching your body to use the arms and legs simultaneously, like in a fight. Because you're moving the body from a vertical plane to a horizontal plane continuously, you're learning balance, agility, and the ability to maneuver while lying on the ground and on your feet. Because of the constant alternating use of the arms and legs, your heart has to work twice as hard as if you just did continuous squats or pushups. This movement will give you great endurance as well as upper and lower body strength. You'll notice that you use jumping movements with the legs, back, abs, and arms in this exercise. This will give you speed and explosiveness throughout the whole body.

I really have been looking at the workout web sites.
Fabulous quanties of information - some in conflict.

However, this site seems to have a pretty balanced approach to workouts and fitness for endurance:http://www.crossfit.com/
Go to the forums and read the posts.

Quite a bit of emphasis on body wieght and gymnastic types of exercises. Combined with some Iron and running.
For an example of the results for a somehat "normal" guy, read this thread from another message board:http://forum.dragondoor.com/training/message/339150/